| Variant ID: vg1219847688 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 19847688 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, G: 0.09, others allele: 0.00, population size: 232. )
AGGAAGAAGATGACACCGAGCTCCAATCTCGCGGCACCAATCAAGGGGTTTCTTGATCCCAACATTGAGGGCAATGCATCCATTTCCCGGTGAACCAGAG[T/G]
ATGAATTCCTCAGTTCACATTTGGAACAGATAGAGGGCGTGCAGGAGAGGCTGTTTGGCGAAGCTAGGAGGTTAAAACATCAAGTCTGCCATGCGGTCTT
AAGACCGCATGGCAGACTTGATGTTTTAACCTCCTAGCTTCGCCAAACAGCCTCTCCTGCACGCCCTCTATCTGTTCCAAATGTGAACTGAGGAATTCAT[A/C]
CTCTGGTTCACCGGGAAATGGATGCATTGCCCTCAATGTTGGGATCAAGAAACCCCTTGATTGGTGCCGCGAGATTGGAGCTCGGTGTCATCTTCTTCCT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.20% | 8.40% | 0.40% | 18.98% | NA |
| All Indica | 2759 | 66.50% | 0.70% | 0.65% | 32.11% | NA |
| All Japonica | 1512 | 81.10% | 18.50% | 0.00% | 0.46% | NA |
| Aus | 269 | 69.50% | 30.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 43.20% | 0.50% | 2.18% | 54.12% | NA |
| Indica II | 465 | 95.90% | 0.60% | 0.00% | 3.44% | NA |
| Indica III | 913 | 58.80% | 0.70% | 0.33% | 40.20% | NA |
| Indica Intermediate | 786 | 75.80% | 0.90% | 0.25% | 23.03% | NA |
| Temperate Japonica | 767 | 69.60% | 30.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 99.20% | 0.40% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 79.70% | 19.50% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 13.30% | 1.11% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1219847688 | T -> DEL | LOC_Os12g32840.1 | N | frameshift_variant | Average:58.435; most accessible tissue: Callus, score: 87.227 | N | N | N | N |
| vg1219847688 | T -> G | LOC_Os12g32840.1 | missense_variant ; p.Tyr10Asp; MODERATE | nonsynonymous_codon ; Y10D | Average:58.435; most accessible tissue: Callus, score: 87.227 | unknown | unknown | TOLERATED | 0.71 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1219847688 | 3.12E-07 | 7.76E-10 | Heading_date | All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1219847688 | NA | 1.19E-09 | Heading_date | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1219847688 | NA | 6.55E-07 | mr1456_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1219847688 | NA | 2.13E-07 | mr1780_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1219847688 | 7.78E-06 | 2.27E-08 | mr1781_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |